/data/results/tools/align/tophat-1.4.0.Linux_x86_64/tophat -p 10 -n 2 -o KO_2h_replicate_I -G /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf -C /data/results/reference/mmu/mm9/bowtie1/mm9c ../fastq/KO_2h_replicate_I.fastq
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/gtf_juncs /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf  > KO_2h_replicate_I/tmp/Mus_musculus.juncs
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/prep_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir KO_2h_replicate_I/ --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --max-mismatches 2 --sam-header KO_2h_replicate_I/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --gtf-annotations /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --gtf-juncs KO_2h_replicate_I/tmp/Mus_musculus.juncs --no-closure-search --no-microexon-search --color --fastq --aux-outfile=KO_2h_replicate_I/left_kept_reads.info ../fastq/KO_2h_replicate_I.fastq | gzip -c - >KO_2h_replicate_I/tmp/left_kept_reads.fq.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/gtf_to_fasta --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir KO_2h_replicate_I/ --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --max-mismatches 2 --sam-header KO_2h_replicate_I/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --gtf-annotations /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --gtf-juncs KO_2h_replicate_I/tmp/Mus_musculus.juncs --no-closure-search --no-microexon-search --color /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf /data/results/reference/mmu/mm9/bowtie1/mm9c.fa KO_2h_replicate_I/tmp/Mus_musculus.NCBIM37.64-toMM9.fa > KO_2h_replicate_I/logs/g2f.out
/data/results/tools/align/bowtie-0.12.9/bowtie-build -C KO_2h_replicate_I/tmp/Mus_musculus.NCBIM37.64-toMM9.fa KO_2h_replicate_I/tmp/Mus_musculus.NCBIM37.64-toMM9
gzip -cd< KO_2h_replicate_I/tmp/left_kept_reads.fq.z|/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends --un KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.fq -v 2 -p 10 -k 60 -m 60 --max /dev/null KO_2h_replicate_I/tmp/Mus_musculus.NCBIM37.64-toMM9 -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/map2gtf --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir KO_2h_replicate_I/ --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --max-mismatches 2 --sam-header KO_2h_replicate_I/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --gtf-annotations /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --gtf-juncs KO_2h_replicate_I/tmp/Mus_musculus.juncs --no-closure-search --no-microexon-search --color /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf KO_2h_replicate_I/tmp/left_kept_reads.m2g.bwtout.z KO_2h_replicate_I/tmp/left_kept_reads.m2g_converted.bam > KO_2h_replicate_I/logs/m2g_left_kept_reads.m2g.out
/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends --un KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_unmapped.fq -v 2 -p 10 -k 20 -m 20 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.fq|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir KO_2h_replicate_I/ --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --max-mismatches 2 --sam-header KO_2h_replicate_I/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --gtf-annotations /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --gtf-juncs KO_2h_replicate_I/tmp/Mus_musculus.juncs --no-closure-search --no-coverage-search --no-microexon-search --color /data/results/reference/mmu/mm9/bowtie1/mm9c.fa KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.fq /dev/null /dev/null /dev/null KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.bwtout.z > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.unspl.bam
gzip -cd< KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1.fq.z|/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends --un KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1_unmapped.fq -v 2 -p 10 -k 40 -m 40 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1.bwtout.z
gzip -cd< KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2.fq.z|/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends --un KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2_unmapped.fq -v 2 -p 10 -k 40 -m 40 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2.bwtout.z
gzip -cd< KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3.fq.z|/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends --un KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3_unmapped.fq -v 2 -p 10 -k 40 -m 40 --max /dev/null /data/results/reference/mmu/mm9/bowtie1/mm9c -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/segment_juncs --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir KO_2h_replicate_I/ --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --max-mismatches 2 --sam-header KO_2h_replicate_I/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --gtf-annotations /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --gtf-juncs KO_2h_replicate_I/tmp/Mus_musculus.juncs --no-closure-search --no-coverage-search --no-microexon-search --color --ium-reads KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1_unmapped.fq,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2_unmapped.fq,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3_unmapped.fq /data/results/reference/mmu/mm9/bowtie1/mm9c.fa KO_2h_replicate_I/tmp/segment.juncs KO_2h_replicate_I/tmp/segment.insertions KO_2h_replicate_I/tmp/segment.deletions KO_2h_replicate_I/tmp/left_kept_reads.fq.z KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.bwtout.z KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1.bwtout.z,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2.bwtout.z,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/juncs_db 3 25 KO_2h_replicate_I/tmp/segment.juncs KO_2h_replicate_I/tmp/segment.insertions KO_2h_replicate_I/tmp/segment.deletions /data/results/reference/mmu/mm9/bowtie1/mm9c.fa
/data/results/tools/align/bowtie-0.12.9/bowtie-build -C KO_2h_replicate_I/tmp/segment_juncs.fa KO_2h_replicate_I/tmp/segment_juncs
gzip -cd< KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1.fq.z|/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends -v 2 -p 10 -k 40 -m 40 --max /dev/null KO_2h_replicate_I/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bwtout.z
gzip -cd< KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2.fq.z|/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends -v 2 -p 10 -k 40 -m 40 --max /dev/null KO_2h_replicate_I/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bwtout.z
gzip -cd< KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3.fq.z|/data/results/tools/align/bowtie-0.12.9/bowtie -q -C --col-keepends -v 2 -p 10 -k 40 -m 40 --max /dev/null KO_2h_replicate_I/tmp/segment_juncs -|/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/fix_map_ordering -|gzip -c > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bwtout.z
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/long_spanning_reads --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir KO_2h_replicate_I/ --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --max-mismatches 2 --sam-header KO_2h_replicate_I/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --gtf-annotations /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --gtf-juncs KO_2h_replicate_I/tmp/Mus_musculus.juncs --no-closure-search --no-coverage-search --no-microexon-search --color /data/results/reference/mmu/mm9/bowtie1/mm9c.fa KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.fq KO_2h_replicate_I/tmp/segment.juncs KO_2h_replicate_I/tmp/segment.insertions KO_2h_replicate_I/tmp/segment.deletions KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1.bwtout.z,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2.bwtout.z,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3.bwtout.z KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg1.to_spliced.bwtout.z,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg2.to_spliced.bwtout.z,KO_2h_replicate_I/tmp/left_kept_reads.m2g_um_seg3.to_spliced.bwtout.z > KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.candidates.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/bam_merge KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.candidates_and_unspl.bam KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.candidates.bam KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.unspl.bam KO_2h_replicate_I/tmp/left_kept_reads.m2g_converted.bam
/mnt/fix/c/solid.data_results.recovered.data/tools/align/tophat-1.4.0.Linux_x86_64/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir KO_2h_replicate_I/ --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --max-mismatches 2 --sam-header KO_2h_replicate_I/tmp/stub_header.sam --max-insertion-length 3 --max-deletion-length 3 -z gzip -p10 --gtf-annotations /data/results/reference/mmu/Mus_musculus.NCBIM37.64-toMM9.gtf --gtf-juncs KO_2h_replicate_I/tmp/Mus_musculus.juncs --no-closure-search --no-coverage-search --no-microexon-search --color --samtools=/data/results/tools/samtools/mysamtools-0.1.19/samtools KO_2h_replicate_I/junctions.bed KO_2h_replicate_I/insertions.bed KO_2h_replicate_I/deletions.bed - KO_2h_replicate_I/tmp/left_kept_reads.m2g_um.candidates_and_unspl.bam KO_2h_replicate_I/tmp/left_kept_reads.fq.z | /data/results/tools/samtools/mysamtools-0.1.19/samtools sort - KO_2h_replicate_I/accepted_hits